TASK-6347 Fix normalization issue in ClinVar #693
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
… clinical variants, #TASK-6347 On branch TASK-6347 Changes to be committed: modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalIndexer.java
…nd Gwas, files to download; and update Cosmic version, #TASK-6347 On branch TASK-6347 Changes to be committed: modified: cellbase-core/src/main/resources/configuration.yml modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/ClinicalDownloadManager.java
…on of the GWAS Catalog, #TASK-6347 On branch TASK-6347 Changes to be committed: modified: cellbase-core/src/main/resources/configuration.yml
…sion, #TASK-6347 On branch TASK-6347 Changes to be committed: modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
On branch TASK-6347 Changes to be committed: modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java
…file; and fix some sonnar issues, #TASK-6347 On branch TASK-6347 Changes to be committed: modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/GwasIndexer.java
j-coll
requested changes
Jun 25, 2024
| try { | ||
| accession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc(); | ||
| } catch (Exception e) { | ||
| logger.warn("Error getting accession\n" + StringUtils.join(e.getStackTrace(), "\n")); |
There was a problem hiding this comment.
Better let the logger to print the stacktrace:
logger.warn("Error getting accession", e);and you can also indicate what will happen with the accession:
logger.warn("Error getting accession. Ignore error and leave accession as null.", e);This applies to all other fields read in this method
| while ((line = inputReader.readLine()) != null) { | ||
| ++lineCounter; | ||
| if (!line.isEmpty()) { | ||
| processedGwasLines++; |
There was a problem hiding this comment.
Might want to use a org.opencb.commons.ProgressLogger here
ProgressLogger progressLogger = new ProgressLogger("Lines parsed").setBatchSize(10000);
...
if (!line.isEmpty() ) {
progressLogger.increment(1);
}There was a problem hiding this comment.
This is just a comment, no action is required (i.e. it's optional)
There was a problem hiding this comment.
Hmm, that's useful, but I can't find a method to get the current number of parsed lines. I need this information to include in the log messages when parsing fails.
There was a problem hiding this comment.
That is very inconvenient... there is no way of obtaining that..
cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/GwasIndexer.java
Show resolved
Hide resolved
cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/GwasIndexer.java
Show resolved
Hide resolved
On branch TASK-6347 Changes to be committed: modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java
j-coll
approved these changes
Jun 25, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
TASK-6347 normalization issue in ClinVar